Configure codex

AGENTS.md

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+
+This project is an R package that transpiles R functions to Fortran.
+
+- To run run the full test suite:
+```sh
+R -q -e 'testthat::test_local()'
+```
+
+- To run a single test file:
+```sh
+R -q -e 'testthat::test_file("tests/testthat/test-dims2f.R")'
+```
+
+- To see the generated C and Fortran code for an R function, use `r2f()`:
+```sh
+R --no-save -q <<'EOF'
+devtools::load_all()
+r2f(function(x) {
+  declare(type(x = double(NA)))
+  x + 1
+})
+EOF
+```
+
+- Never disable or skip tests.

scripts/setup_codex.sh

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+#!/usr/bin/env bash
+#
+# This script sets up the openai/codex-universal docker image
+# with everything needed to run quickr tests.
+# Run this script as the "Setup script" when configuring an environment in
+# https://chatgpt.com/codex/settings/environments,
+#  ./scripts/setup_codex.sh
+#
+# More info:
+# https://platform.openai.com/docs/codex/overview#default-universal-image
+
+set -eo pipefail
+
+
+if ! grep -q 'NOT_CRAN=true' ~/.bashrc; then
+  echo 'export NOT_CRAN=true' >> ~/.bashrc
+fi
+
+export DEBIAN_FRONTEND=noninteractive
+
+### --- setup instructions from https://cran.r-project.org/bin/linux/ubuntu/#root ----
+# update indices
+apt update -qq
+# install two helper packages we need
+apt install -y --no-install-recommends software-properties-common dirmngr
+# add the signing key (by Michael Rutter) for these repos
+# To verify key, run gpg --show-keys /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
+# Fingerprint: E298A3A825C0D65DFD57CBB651716619E084DAB9
+wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
+# add the repo from CRAN -- lsb_release adjusts to 'noble' or 'jammy' or ... as needed
+add-apt-repository -y "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
+# install R itself
+sudo apt install -y --no-install-recommends r-base
+### --- end setup instructions from https://cran.r-project.org/bin/linux/ubuntu/#root ----
+
+
+### --- https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh ---
+### lightly modified to avoid using gpg, which doesn't use up the codex proxy correctly and errors
+#!/bin/bash
+
+## See the README.md of 'r2u' for details on these steps
+##
+## This script has been tested on a plain and minimal ubuntu:24.04
+##
+## On a well-connected machine this script should take well under one minute
+##
+## Note that you need to run this as root, or run the whole script via sudo
+## To run individual commands as root, prefix each command with sudo and use
+## 'echo | sudo tee file' as the command before the EOF redirect statement
+
+set -eu
+
+## First: update apt and get keys
+apt update -qq && apt install --yes --no-install-recommends ca-certificates gnupg
+## use gpg directly instead of the now-deprecated apt-key command
+# gpg --homedir /tmp --no-default-keyring --keyring /usr/share/keyrings/r2u.gpg --keyserver keyserver.ubuntu.com --recv-keys A1489FE2AB99A21A 67C2D66C4B1D4339 51716619E084DAB9
+wget -q -O- https://eddelbuettel.github.io/r2u/assets/dirk_eddelbuettel_key.asc \
+    | tee -a /etc/apt/trusted.gpg.d/cranapt_key.asc
+
+## Second: add the repo -- here we use the well-connected mirror
+echo > /etc/apt/sources.list.d/r2u.sources <<EOF
+Types: deb
+URIs: https://r2u.stat.illinois.edu/ubuntu
+Suites: noble
+Components: main
+Arch: amd64, arm64
+Signed-By: /usr/share/keyrings/r2u.gpg
+EOF
+
+## Third: ensure current R is used
+echo > /etc/apt/sources.list.d/cran.sources <<EOF
+Types: deb
+URIs: https://cloud.r-project.org/bin/linux/ubuntu
+Suites: noble-cran40/
+Components:
+Arch: amd64, arm64
+Signed-By: /usr/share/keyrings/r2u.gpg
+EOF
+apt update -qq
+DEBIAN_FRONTEND=noninteractive apt install --yes --no-install-recommends r-base-core
+
+## Fourth: add pinning to ensure package sorting
+echo > /etc/apt/preferences.d/99cranapt <<EOF
+Package: *
+Pin: release o=CRAN-Apt Project
+Pin: release l=CRAN-Apt Packages
+Pin-Priority: 700
+EOF
+
+## Fifth: install bspm (and its Python requirements) and enable it
+## If needed (in bare container, say) install python tools for bspm and R itself
+apt install --yes --no-install-recommends python3-{dbus,gi,apt} make
+## Then install bspm (as root) and enable it, and enable a speed optimization
+Rscript -e 'install.packages("bspm")'
+echo >> /etc/R/Rprofile.site <<EOF
+suppressMessages(bspm::enable())
+options(bspm.version.check=FALSE)
+EOF
+
+# Done!
+
+### ---- END https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh ---
+
+### Now setup the actual dependencies for the quirckr package
+
+apt-get install -y gfortran gcc
+apt-get install -y --no-install-recommends r-cran-{glue,testthat}
+# apt-get install -y --no-install-recommends r-cran-{dotty,s7}  ## not available on r2u noble ??
+R -q -e 'install.packages(c("dotty", "S7"))'
+apt-get install -y --no-install-recommends r-cran-devtools  # not strictly necessary, but pulls in load_all(), cli, ...
+
+
+
+echo >> ~/.Rprofile <<'EOF'
+options(
+  testthat.use_colours = FALSE, Should the output be coloured? (Default: TRUE).
+  # testthat.summary.max_reports: The maximum number of detailed test reports printed for the summary reporter (default: 10).
+  testthat.summary.omit_dots = TRUE
+)
+EOF
+
+# R -e 'devtools::test()'